Comprehensive functional analyses of expressed sequence tags in common wheat (Triticum aestivum).

DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes
Alagu ManickaveluYasunari Ogihara

Abstract

About 1 million expressed sequence tag (EST) sequences comprising 125.3 Mb nucleotides were accreted from 51 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including abiotic stresses and pathogen challenges in common wheat (Triticum aestivum). Expressed sequence tags were assembled with stringent parameters after processing with inbuild scripts, resulting in 37,138 contigs and 215,199 singlets. In the assembled sequences, 10.6% presented no matches with existing sequences in public databases. Functional characterization of wheat unigenes by gene ontology annotation, mining transcription factors, full-length cDNA, and miRNA targeting sites were carried out. A bioinformatics strategy was developed to discover single-nucleotide polymorphisms (SNPs) within our large EST resource and reported the SNPs between and within (homoeologous) cultivars. Digital gene expression was performed to find the tissue-specific gene expression, and correspondence analysis was executed to identify common and specific gene expression by selecting four biotic stress-related libraries. The assembly and associated information cater a framework for future investigation in functional genomics.

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Citations

Mar 19, 2013·Journal of Molecular Evolution·E K KhlestkinaE A Salina
May 11, 2013·Database : the Journal of Biological Databases and Curation·Jonathan VincentPierre Martre
Apr 22, 2014·Molecular Genetics and Genomics : MGG·Sezer OkayTurgay Unver
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Jul 11, 2019·International Journal of Molecular Sciences·Shahbaz KhanZhi-Qiang Gao
Mar 28, 2018·International Journal of Genomics·Lingjie MaZhengqiang Ma
Aug 19, 2021·Functional & Integrative Genomics·Kazuhiro SatoShigeo Takumi

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Methods Mentioned

BETA
transgenic
cDNA
genotyping

Software Mentioned

perl
Tablet
RAP
BLASTN
CAP3
script
PHRED
InterProScan
scripts
BLASTX

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